Sphinx is a protein loop modelling algorithm that combines knowledge-based and ab initio approaches. Given a protein structure, location of the loop to be modelled and the sequence of that loop, it searches a database of fragments for sections of other proteins that are shorter than the target loop, but that may have some structural similarity. By using ab initio techniques, the loop conformations can be made to be the correct length. Once a set of conformations has been produced, a fast statistical potential is used to cull the set to only 500 structures, which are then scored using SOAP-Loop (Dong et al., 2013) to produce a ranking.
If you'd rather use the H3-specific Sphinx, please click here.
If you are not sure how to use Sphinx, please look at the submission guidelines here.
If you would like to see what kind of results you can expect, please see here.
If you have not already done so, we recommend first running FREAD, a knowledge-based algorithm which can also produce accurate predictions but requires less computation time. It can be found here.For a full description of the pipeline, or if you use this software, please refer to:
Marks, Cet al. Sphinx: Merging knowledge-based and ab initio approaches to improve protein loop prediction. Bioinformatics. (2017)
Current Jobs Queue
Currently running 0 job(s). Max permitted is 20
|Job ID||Job type||Submission time||Status|
|SEJ (?)||SphinxH3||Friday 21st of September 2018 07:08:13 AM||Failed|
|SEJ (?)||Sphinx||Monday 17th of September 2018 06:01:34 PM||Done|
|SEJ (?)||SphinxH3||Monday 17th of September 2018 05:11:10 PM||Done|
|SEJ (?)||SphinxH3||Thursday 13th of September 2018 01:39:28 PM||Done|
|SEJ (?)||SphinxH3||Thursday 13th of September 2018 12:42:49 PM||Done|
|SEJ (?)||SphinxH3||Thursday 13th of September 2018 10:12:07 AM||Done|
|SEJ (?)||SphinxH3||Thursday 13th of September 2018 09:40:46 AM||Done|
|SEJ (?)||SphinxH3||Monday 3rd of September 2018 06:10:21 PM||Failed|
|SEJ (?)||SphinxH3||Thursday 23rd of August 2018 10:38:32 AM||Done|